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Abstract

Tropical smallholder agriculture is undergoing rapid transformation in nutrient cycling
pathways as international development efforts strongly promote greater use of mineral
fertilizers to increase crop yields. These changes in nutrient availability may alter
the composition of microbial communities with consequences for rates of biogeochemical
processes that control nutrient losses to the environment. Ecological theory suggests
that altered microbial diversity will strongly influence processes performed by relatively
few microbial taxa, such as denitrification and hence nitrogen losses as nitrous oxide,
a powerful greenhouse gas. Whether this theory helps predict nutrient losses from
agriculture depends on the relative effects of microbial community change and increased
nutrient availability on ecosystem processes. We find that mineral and organic nutrient
addition to smallholder farms in Kenya alters the taxonomic and functional diversity
of soil microbes. However, we find that the direct effects of farm management on both
denitrification and carbon mineralization are greater than indirect effects through
changes in the taxonomic and functional diversity of microbial communities. Changes
in functional diversity are strongly coupled to changes in specific functional genes
involved in denitrification, suggesting that it is the expression, rather than abundance,
of key functional genes that can serve as an indicator of ecosystem process rates.
Our results thus suggest that widely used broad summary statistics of microbial diversity
based on DNA may be inappropriate for linking microbial communities to ecosystem processes
in certain applied settings. Our results also raise doubts about the relative control
of microbial composition compared to direct effects of management on nutrient losses
in applied settings such as tropical agriculture.

DNA sequencing continues to decrease in cost with the Illumina HiSeq2000 generating up to 600 Gb of paired-end 100 base reads in a ten-day run. Here we present a protocol for community amplicon sequencing on the HiSeq2000 and MiSeq Illumina platforms, and apply that protocol to sequence 24 microbial communities from host-associated and free-living environments. A critical question as more sequencing platforms become available is whether biological conclusions derived on one platform are consistent with what would be derived on a different platform. We show that the protocol developed for these instruments successfully recaptures known biological results, and additionally that biological conclusions are consistent across sequencing platforms (the HiSeq2000 versus the MiSeq) and across the sequenced regions of amplicons.

Increasing population and consumption are placing unprecedented demands on agriculture and natural resources. Today, approximately a billion people are chronically malnourished while our agricultural systems are concurrently degrading land, water, biodiversity and climate on a global scale. To meet the world's future food security and sustainability needs, food production must grow substantially while, at the same time, agriculture's environmental footprint must shrink dramatically. Here we analyse solutions to this dilemma, showing that tremendous progress could be made by halting agricultural expansion, closing 'yield gaps' on underperforming lands, increasing cropping efficiency, shifting diets and reducing waste. Together, these strategies could double food production while greatly reducing the environmental impacts of agriculture.

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